Data

scRNA-seq data was captured from the bone marrow mononuclear cells of two patients with leukemia before and after undergoing a hematopoietic stem cell transplant. We subjected the cells from each patient to various dimensionality reduction techniques to determine whether they are capable of distinguishing the treatment states of the cells. scRNA-seq data from two healthy controls are used to perform cPCA and scPCA.

AML027

PCA

cPCA

scPCA

Analysis of Genes with Non-Zero Entries in Loadings Matrix

The following table provides the gene symbol and loadings of the genes with non-zero entries in one of the loadings vectors of the first two scPCs.

## # A tibble: 3 x 3
##   gene_sym    scPC1 scPC2
##   <chr>       <dbl> <dbl>
## 1 STMN1     -0.997      0
## 2 LINC00152  0.0732     0
## 3 PDLIM1     0         -1

Comparison of Loadings Weights: cPCA and scPCA

The absolute valules of the loadings are not compared for this patient, since only three entries in the leading loadings vectors produced by scPCA are non-zero.

t-SNE

UMAP

ZINB-WaVE

Combined Plots

AML035

PCA

cPCA

scPCA

Analysis of Genes with Non-Zero Entries in Loadings Matrix

The following table provides the gene symbol and loadings of the genes with non-zero entries in one of the loadings vectors of the first two scPCs.

## # A tibble: 177 x 3
##    gene_sym     scPC1  scPC2
##    <chr>        <dbl>  <dbl>
##  1 HBB      -0.0612    0.697
##  2 HBA2      0        -0.114
##  3 HBA1      0.0957   -0.680
##  4 TMSB4X   -0.000835  0    
##  5 RPL10     0.0176    0    
##  6 RPLP1    -0.00289   0    
##  7 RPL13    -0.0317    0    
##  8 RPL13A   -0.0322    0    
##  9 RPS4X    -0.0805    0    
## 10 MALAT1    0.00873   0    
## # … with 167 more rows

Comparison of Loadings Weights: cPCA and scPCA

t-SNE

UMAP

ZINB-WaVE

Combined Plots